Ben Bolstad
| Snapshot Date: 2025-12-08 13:45 -0500 (Mon, 08 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_22 |
| git_last_commit: d2ce144 |
| git_last_commit_date: 2025-10-29 09:58:55 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-11 12:03 -0500 (Thu, 11 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4670 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4604 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 257/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.74.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.74.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BufferedMatrix_1.74.0.tar.gz |
| StartedAt: 2025-12-08 21:41:32 -0500 (Mon, 08 Dec 2025) |
| EndedAt: 2025-12-08 21:41:56 -0500 (Mon, 08 Dec 2025) |
| EllapsedTime: 24.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BufferedMatrix_1.74.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.74.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BufferedMatrix’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup?
209 | $x^{power}$ elementwise of the matrix
| ^
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘Rcodetesting.R’
Running ‘c_code_level_tests.R’
Running ‘objectTesting.R’
Running ‘rawCalltesting.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.74.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function ‘dbm_ReadOnlyMode’:
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: ‘sort_double’ defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init_package.c -o init_package.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘rowSums’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colSums’ in package ‘BufferedMatrix’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘BufferedMatrix’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘BufferedMatrix’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix", "BufferedMatrix", .libPaths());.C("dbm_c_tester",integer(1))
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
Adding Additional Column
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000
Reassigning values
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 3
Buffer Cols: 3
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Activating Row Buffer
In row mode: 1
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Squaring Last Column
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
5.000000 10.000000 15.000000 20.000000 25.000000 900.000000
Square rooting Last Row, then turing off Row Buffer
In row mode: 0
Checking on value that should be not be in column buffer2.236068
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
2.236068 3.162278 3.872983 4.472136 5.000000 30.000000
Single Indexing. Assign each value its square
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Resizing Buffers Smaller
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Activating Row Mode.
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
Activating ReadOnly Mode.
The results of assignment is: 0
Printing matrix reversed.
900.000000 625.000000 400.000000 225.000000 100.000000 25.000000
841.000000 576.000000 361.000000 196.000000 81.000000 16.000000
784.000000 529.000000 324.000000 169.000000 64.000000 9.000000
729.000000 484.000000 289.000000 144.000000 49.000000 -30.000000
676.000000 441.000000 256.000000 121.000000 -20.000000 -10.000000
[[1]]
[1] 0
>
> proc.time()
user system elapsed
0.244 0.045 0.280
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 478284 25.6 1046725 56 639600 34.2
Vcells 884773 6.8 8388608 64 2081613 15.9
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Mon Dec 8 21:41:47 2025"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Mon Dec 8 21:41:47 2025"
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
>
>
> RowMode(tmp2)
<pointer: 0x5ff3d754f370>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Mon Dec 8 21:41:47 2025"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Mon Dec 8 21:41:47 2025"
>
> ColMode(tmp2)
<pointer: 0x5ff3d754f370>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.218368 0.52871129 -1.1748324 -0.07478941
[2,] -1.936538 -0.04890691 -0.5578186 -1.31911808
[3,] -0.996419 -0.38902896 0.4243276 1.44484167
[4,] 1.300824 -2.51349491 -0.7019406 0.04372754
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.218368 0.52871129 1.1748324 0.07478941
[2,] 1.936538 0.04890691 0.5578186 1.31911808
[3,] 0.996419 0.38902896 0.4243276 1.44484167
[4,] 1.300824 2.51349491 0.7019406 0.04372754
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.0109125 0.7271254 1.0838969 0.2734765
[2,] 1.3915956 0.2211491 0.7468725 1.1485287
[3,] 0.9982079 0.6237219 0.6514043 1.2020157
[4,] 1.1405367 1.5854006 0.8378190 0.2091113
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 225.32749 32.79996 37.01380 27.80955
[2,] 40.85249 27.26040 33.02654 37.80440
[3,] 35.97850 31.62625 31.93837 38.46500
[4,] 37.70619 43.36750 34.08013 27.13484
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x5ff3d86af800>
> exp(tmp5)
<pointer: 0x5ff3d86af800>
> log(tmp5,2)
<pointer: 0x5ff3d86af800>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 468.9897
> Min(tmp5)
[1] 53.4469
> mean(tmp5)
[1] 72.57445
> Sum(tmp5)
[1] 14514.89
> Var(tmp5)
[1] 871.9651
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 90.19688 71.08644 70.15364 71.06266 69.23762 71.74750 70.47437 69.73049
[9] 65.53197 76.52295
> rowSums(tmp5)
[1] 1803.938 1421.729 1403.073 1421.253 1384.752 1434.950 1409.487 1394.610
[9] 1310.639 1530.459
> rowVars(tmp5)
[1] 8034.87932 95.60632 74.35710 104.90489 65.81452 67.88490
[7] 72.06079 56.06096 51.36141 77.74242
> rowSd(tmp5)
[1] 89.637488 9.777849 8.623056 10.242309 8.112615 8.239229 8.488863
[8] 7.487387 7.166688 8.817166
> rowMax(tmp5)
[1] 468.98965 86.87533 89.14691 90.26377 87.10558 89.03076 88.06140
[8] 91.12016 81.00706 90.28755
> rowMin(tmp5)
[1] 54.83915 56.14745 57.47535 53.72699 57.34030 58.87733 53.44690 56.32366
[9] 54.11302 59.00589
>
> colMeans(tmp5)
[1] 112.83290 70.22909 70.98440 69.37350 67.31477 72.36181 68.92413
[8] 68.39491 73.75409 71.38444 67.29388 72.44878 64.59349 72.86156
[15] 73.41487 67.19371 72.16622 75.03509 67.21409 73.71333
> colSums(tmp5)
[1] 1128.3290 702.2909 709.8440 693.7350 673.1477 723.6181 689.2413
[8] 683.9491 737.5409 713.8444 672.9388 724.4878 645.9349 728.6156
[15] 734.1487 671.9371 721.6622 750.3509 672.1409 737.1333
> colVars(tmp5)
[1] 15721.32015 119.46231 51.29172 94.00027 83.41262 38.29666
[7] 70.05160 37.55478 67.50857 79.75418 44.20658 62.99459
[13] 57.07296 146.34609 122.14726 42.65708 187.92360 63.39126
[19] 49.95327 76.41897
> colSd(tmp5)
[1] 125.384689 10.929882 7.161824 9.695374 9.133051 6.188430
[7] 8.369684 6.128196 8.216360 8.930520 6.648803 7.936913
[13] 7.554665 12.097359 11.052025 6.531239 13.708523 7.961863
[19] 7.067763 8.741795
> colMax(tmp5)
[1] 468.98965 90.26377 81.90936 80.67166 82.98888 84.46230 81.12241
[8] 75.69504 86.19983 85.62437 75.00617 89.02097 78.92500 90.28755
[15] 87.10558 78.64053 91.12016 86.69275 77.41501 86.04284
> colMin(tmp5)
[1] 57.34030 56.73895 57.68065 56.47762 56.14745 67.14335 54.11302 59.24291
[9] 60.41016 58.94729 53.72699 64.79448 54.83915 53.44690 59.00589 55.79025
[17] 56.71387 60.38062 58.63355 58.44160
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 90.19688 71.08644 70.15364 71.06266 69.23762 71.74750 70.47437 69.73049
[9] NA 76.52295
> rowSums(tmp5)
[1] 1803.938 1421.729 1403.073 1421.253 1384.752 1434.950 1409.487 1394.610
[9] NA 1530.459
> rowVars(tmp5)
[1] 8034.87932 95.60632 74.35710 104.90489 65.81452 67.88490
[7] 72.06079 56.06096 47.48896 77.74242
> rowSd(tmp5)
[1] 89.637488 9.777849 8.623056 10.242309 8.112615 8.239229 8.488863
[8] 7.487387 6.891223 8.817166
> rowMax(tmp5)
[1] 468.98965 86.87533 89.14691 90.26377 87.10558 89.03076 88.06140
[8] 91.12016 NA 90.28755
> rowMin(tmp5)
[1] 54.83915 56.14745 57.47535 53.72699 57.34030 58.87733 53.44690 56.32366
[9] NA 59.00589
>
> colMeans(tmp5)
[1] 112.83290 70.22909 70.98440 69.37350 67.31477 72.36181 68.92413
[8] 68.39491 NA 71.38444 67.29388 72.44878 64.59349 72.86156
[15] 73.41487 67.19371 72.16622 75.03509 67.21409 73.71333
> colSums(tmp5)
[1] 1128.3290 702.2909 709.8440 693.7350 673.1477 723.6181 689.2413
[8] 683.9491 NA 713.8444 672.9388 724.4878 645.9349 728.6156
[15] 734.1487 671.9371 721.6622 750.3509 672.1409 737.1333
> colVars(tmp5)
[1] 15721.32015 119.46231 51.29172 94.00027 83.41262 38.29666
[7] 70.05160 37.55478 NA 79.75418 44.20658 62.99459
[13] 57.07296 146.34609 122.14726 42.65708 187.92360 63.39126
[19] 49.95327 76.41897
> colSd(tmp5)
[1] 125.384689 10.929882 7.161824 9.695374 9.133051 6.188430
[7] 8.369684 6.128196 NA 8.930520 6.648803 7.936913
[13] 7.554665 12.097359 11.052025 6.531239 13.708523 7.961863
[19] 7.067763 8.741795
> colMax(tmp5)
[1] 468.98965 90.26377 81.90936 80.67166 82.98888 84.46230 81.12241
[8] 75.69504 NA 85.62437 75.00617 89.02097 78.92500 90.28755
[15] 87.10558 78.64053 91.12016 86.69275 77.41501 86.04284
> colMin(tmp5)
[1] 57.34030 56.73895 57.68065 56.47762 56.14745 67.14335 54.11302 59.24291
[9] NA 58.94729 53.72699 64.79448 54.83915 53.44690 59.00589 55.79025
[17] 56.71387 60.38062 58.63355 58.44160
>
> Max(tmp5,na.rm=TRUE)
[1] 468.9897
> Min(tmp5,na.rm=TRUE)
[1] 53.4469
> mean(tmp5,na.rm=TRUE)
[1] 72.55595
> Sum(tmp5,na.rm=TRUE)
[1] 14438.63
> Var(tmp5,na.rm=TRUE)
[1] 876.3002
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.19688 71.08644 70.15364 71.06266 69.23762 71.74750 70.47437 69.73049
[9] 64.96753 76.52295
> rowSums(tmp5,na.rm=TRUE)
[1] 1803.938 1421.729 1403.073 1421.253 1384.752 1434.950 1409.487 1394.610
[9] 1234.383 1530.459
> rowVars(tmp5,na.rm=TRUE)
[1] 8034.87932 95.60632 74.35710 104.90489 65.81452 67.88490
[7] 72.06079 56.06096 47.48896 77.74242
> rowSd(tmp5,na.rm=TRUE)
[1] 89.637488 9.777849 8.623056 10.242309 8.112615 8.239229 8.488863
[8] 7.487387 6.891223 8.817166
> rowMax(tmp5,na.rm=TRUE)
[1] 468.98965 86.87533 89.14691 90.26377 87.10558 89.03076 88.06140
[8] 91.12016 81.00706 90.28755
> rowMin(tmp5,na.rm=TRUE)
[1] 54.83915 56.14745 57.47535 53.72699 57.34030 58.87733 53.44690 56.32366
[9] 54.11302 59.00589
>
> colMeans(tmp5,na.rm=TRUE)
[1] 112.83290 70.22909 70.98440 69.37350 67.31477 72.36181 68.92413
[8] 68.39491 73.47606 71.38444 67.29388 72.44878 64.59349 72.86156
[15] 73.41487 67.19371 72.16622 75.03509 67.21409 73.71333
> colSums(tmp5,na.rm=TRUE)
[1] 1128.3290 702.2909 709.8440 693.7350 673.1477 723.6181 689.2413
[8] 683.9491 661.2845 713.8444 672.9388 724.4878 645.9349 728.6156
[15] 734.1487 671.9371 721.6622 750.3509 672.1409 737.1333
> colVars(tmp5,na.rm=TRUE)
[1] 15721.32015 119.46231 51.29172 94.00027 83.41262 38.29666
[7] 70.05160 37.55478 75.07751 79.75418 44.20658 62.99459
[13] 57.07296 146.34609 122.14726 42.65708 187.92360 63.39126
[19] 49.95327 76.41897
> colSd(tmp5,na.rm=TRUE)
[1] 125.384689 10.929882 7.161824 9.695374 9.133051 6.188430
[7] 8.369684 6.128196 8.664728 8.930520 6.648803 7.936913
[13] 7.554665 12.097359 11.052025 6.531239 13.708523 7.961863
[19] 7.067763 8.741795
> colMax(tmp5,na.rm=TRUE)
[1] 468.98965 90.26377 81.90936 80.67166 82.98888 84.46230 81.12241
[8] 75.69504 86.19983 85.62437 75.00617 89.02097 78.92500 90.28755
[15] 87.10558 78.64053 91.12016 86.69275 77.41501 86.04284
> colMin(tmp5,na.rm=TRUE)
[1] 57.34030 56.73895 57.68065 56.47762 56.14745 67.14335 54.11302 59.24291
[9] 60.41016 58.94729 53.72699 64.79448 54.83915 53.44690 59.00589 55.79025
[17] 56.71387 60.38062 58.63355 58.44160
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.19688 71.08644 70.15364 71.06266 69.23762 71.74750 70.47437 69.73049
[9] NaN 76.52295
> rowSums(tmp5,na.rm=TRUE)
[1] 1803.938 1421.729 1403.073 1421.253 1384.752 1434.950 1409.487 1394.610
[9] 0.000 1530.459
> rowVars(tmp5,na.rm=TRUE)
[1] 8034.87932 95.60632 74.35710 104.90489 65.81452 67.88490
[7] 72.06079 56.06096 NA 77.74242
> rowSd(tmp5,na.rm=TRUE)
[1] 89.637488 9.777849 8.623056 10.242309 8.112615 8.239229 8.488863
[8] 7.487387 NA 8.817166
> rowMax(tmp5,na.rm=TRUE)
[1] 468.98965 86.87533 89.14691 90.26377 87.10558 89.03076 88.06140
[8] 91.12016 NA 90.28755
> rowMin(tmp5,na.rm=TRUE)
[1] 54.83915 56.14745 57.47535 53.72699 57.34030 58.87733 53.44690 56.32366
[9] NA 59.00589
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 117.49577 70.54393 72.46259 69.66367 68.35743 72.26945 70.56981
[8] 69.14505 NaN 72.50840 67.93534 71.49786 64.94116 73.65957
[15] 74.12374 66.73541 73.85229 75.25924 67.25744 75.38480
> colSums(tmp5,na.rm=TRUE)
[1] 1057.4619 634.8953 652.1633 626.9730 615.2168 650.4251 635.1283
[8] 622.3054 0.0000 652.5756 611.4181 643.4807 584.4704 662.9361
[15] 667.1137 600.6187 664.6706 677.3331 605.3170 678.4632
> colVars(tmp5,na.rm=TRUE)
[1] 17441.88390 133.27999 33.12131 104.80308 81.60900 42.98778
[7] 48.34015 35.91866 NA 75.51140 45.10326 60.69612
[13] 62.84727 157.47519 131.76247 45.62626 179.43213 70.74994
[19] 56.17628 54.54075
> colSd(tmp5,na.rm=TRUE)
[1] 132.067725 11.544695 5.755111 10.237337 9.033770 6.556507
[7] 6.952708 5.993218 NA 8.689730 6.715896 7.790772
[13] 7.927627 12.548912 11.478783 6.754721 13.395228 8.411299
[19] 7.495084 7.385171
> colMax(tmp5,na.rm=TRUE)
[1] 468.98965 90.26377 81.90936 80.67166 82.98888 84.46230 81.12241
[8] 75.69504 -Inf 85.62437 75.00617 89.02097 78.92500 90.28755
[15] 87.10558 78.64053 91.12016 86.69275 77.41501 86.04284
> colMin(tmp5,na.rm=TRUE)
[1] 57.34030 56.73895 64.54488 56.47762 56.14745 67.14335 58.58090 59.24291
[9] Inf 58.94729 53.72699 64.79448 54.83915 53.44690 59.00589 55.79025
[17] 56.71387 60.38062 58.63355 58.44160
>
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 3
> which.col <- 1
> cat(which.row," ",which.col,"\n")
3 1
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> rowVars(tmp5,na.rm=TRUE)
[1] 133.44958 132.54832 281.66249 175.37555 292.91609 144.08900 198.45247
[8] 202.87653 91.42233 319.30792
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 133.44958 132.54832 281.66249 175.37555 292.91609 144.08900 198.45247
[8] 202.87653 91.42233 319.30792
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] -5.684342e-14 5.684342e-14 1.136868e-13 4.263256e-14 0.000000e+00
[6] -1.705303e-13 -2.273737e-13 0.000000e+00 0.000000e+00 1.136868e-13
[11] 2.273737e-13 1.705303e-13 -5.684342e-14 -8.526513e-14 1.136868e-13
[16] 0.000000e+00 1.705303e-13 8.526513e-14 1.136868e-13 -5.684342e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
3 19
1 14
1 5
10 13
2 9
8 11
5 7
5 16
9 1
2 18
8 9
9 7
6 1
3 16
1 16
10 17
9 4
1 20
1 10
7 10
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 4.427062
> Min(tmp)
[1] -1.914464
> mean(tmp)
[1] 0.04492234
> Sum(tmp)
[1] 4.492234
> Var(tmp)
[1] 1.07554
>
> rowMeans(tmp)
[1] 0.04492234
> rowSums(tmp)
[1] 4.492234
> rowVars(tmp)
[1] 1.07554
> rowSd(tmp)
[1] 1.037082
> rowMax(tmp)
[1] 4.427062
> rowMin(tmp)
[1] -1.914464
>
> colMeans(tmp)
[1] -0.35372554 -0.29007026 0.92554368 0.05556540 -1.02160988 -0.28154309
[7] -0.41064711 -0.46217719 -0.90785963 0.73112971 1.15118884 -0.23025444
[13] 0.82961279 4.42706155 2.00054918 -0.07003976 1.06148460 -1.60164257
[19] 0.13148942 0.71655102 1.83470161 -0.54355468 -0.07714368 -1.27157085
[25] -0.07535437 0.64532799 -0.23313105 1.39806869 0.92995469 -0.85128543
[31] 0.03657897 -1.06443463 -0.55840876 1.48287246 1.01953658 -1.91446436
[37] -0.18670163 -0.98494413 0.16089328 -0.45468447 0.50127449 -0.37578400
[43] -0.29116869 -1.53967119 0.25345017 0.35654935 -1.27121415 1.47820134
[49] -1.61020436 0.30443821 -0.58313458 1.32726755 1.20490422 1.46760953
[55] -1.45343125 -0.39679665 0.56990150 -1.47876553 -0.25635019 1.08194751
[61] 0.75527462 0.69298218 0.44359033 -0.91849082 0.63404576 -0.11154952
[67] -0.45571389 1.59266502 -0.38776095 -0.90121392 0.47106856 -0.31658369
[73] -0.64509246 0.63684779 0.83135077 0.52097225 1.30052020 -1.29865737
[79] -1.10895747 -0.17772828 0.33130899 0.53367063 -1.21314430 0.21733394
[85] -1.53105147 -0.35777755 -0.56094823 0.36383418 0.40418018 0.80473376
[91] -1.02523060 -0.10855403 -1.41212023 0.29152993 -1.65252739 0.32476861
[97] 1.76232428 -0.79342918 -0.46907805 2.04295520
> colSums(tmp)
[1] -0.35372554 -0.29007026 0.92554368 0.05556540 -1.02160988 -0.28154309
[7] -0.41064711 -0.46217719 -0.90785963 0.73112971 1.15118884 -0.23025444
[13] 0.82961279 4.42706155 2.00054918 -0.07003976 1.06148460 -1.60164257
[19] 0.13148942 0.71655102 1.83470161 -0.54355468 -0.07714368 -1.27157085
[25] -0.07535437 0.64532799 -0.23313105 1.39806869 0.92995469 -0.85128543
[31] 0.03657897 -1.06443463 -0.55840876 1.48287246 1.01953658 -1.91446436
[37] -0.18670163 -0.98494413 0.16089328 -0.45468447 0.50127449 -0.37578400
[43] -0.29116869 -1.53967119 0.25345017 0.35654935 -1.27121415 1.47820134
[49] -1.61020436 0.30443821 -0.58313458 1.32726755 1.20490422 1.46760953
[55] -1.45343125 -0.39679665 0.56990150 -1.47876553 -0.25635019 1.08194751
[61] 0.75527462 0.69298218 0.44359033 -0.91849082 0.63404576 -0.11154952
[67] -0.45571389 1.59266502 -0.38776095 -0.90121392 0.47106856 -0.31658369
[73] -0.64509246 0.63684779 0.83135077 0.52097225 1.30052020 -1.29865737
[79] -1.10895747 -0.17772828 0.33130899 0.53367063 -1.21314430 0.21733394
[85] -1.53105147 -0.35777755 -0.56094823 0.36383418 0.40418018 0.80473376
[91] -1.02523060 -0.10855403 -1.41212023 0.29152993 -1.65252739 0.32476861
[97] 1.76232428 -0.79342918 -0.46907805 2.04295520
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] -0.35372554 -0.29007026 0.92554368 0.05556540 -1.02160988 -0.28154309
[7] -0.41064711 -0.46217719 -0.90785963 0.73112971 1.15118884 -0.23025444
[13] 0.82961279 4.42706155 2.00054918 -0.07003976 1.06148460 -1.60164257
[19] 0.13148942 0.71655102 1.83470161 -0.54355468 -0.07714368 -1.27157085
[25] -0.07535437 0.64532799 -0.23313105 1.39806869 0.92995469 -0.85128543
[31] 0.03657897 -1.06443463 -0.55840876 1.48287246 1.01953658 -1.91446436
[37] -0.18670163 -0.98494413 0.16089328 -0.45468447 0.50127449 -0.37578400
[43] -0.29116869 -1.53967119 0.25345017 0.35654935 -1.27121415 1.47820134
[49] -1.61020436 0.30443821 -0.58313458 1.32726755 1.20490422 1.46760953
[55] -1.45343125 -0.39679665 0.56990150 -1.47876553 -0.25635019 1.08194751
[61] 0.75527462 0.69298218 0.44359033 -0.91849082 0.63404576 -0.11154952
[67] -0.45571389 1.59266502 -0.38776095 -0.90121392 0.47106856 -0.31658369
[73] -0.64509246 0.63684779 0.83135077 0.52097225 1.30052020 -1.29865737
[79] -1.10895747 -0.17772828 0.33130899 0.53367063 -1.21314430 0.21733394
[85] -1.53105147 -0.35777755 -0.56094823 0.36383418 0.40418018 0.80473376
[91] -1.02523060 -0.10855403 -1.41212023 0.29152993 -1.65252739 0.32476861
[97] 1.76232428 -0.79342918 -0.46907805 2.04295520
> colMin(tmp)
[1] -0.35372554 -0.29007026 0.92554368 0.05556540 -1.02160988 -0.28154309
[7] -0.41064711 -0.46217719 -0.90785963 0.73112971 1.15118884 -0.23025444
[13] 0.82961279 4.42706155 2.00054918 -0.07003976 1.06148460 -1.60164257
[19] 0.13148942 0.71655102 1.83470161 -0.54355468 -0.07714368 -1.27157085
[25] -0.07535437 0.64532799 -0.23313105 1.39806869 0.92995469 -0.85128543
[31] 0.03657897 -1.06443463 -0.55840876 1.48287246 1.01953658 -1.91446436
[37] -0.18670163 -0.98494413 0.16089328 -0.45468447 0.50127449 -0.37578400
[43] -0.29116869 -1.53967119 0.25345017 0.35654935 -1.27121415 1.47820134
[49] -1.61020436 0.30443821 -0.58313458 1.32726755 1.20490422 1.46760953
[55] -1.45343125 -0.39679665 0.56990150 -1.47876553 -0.25635019 1.08194751
[61] 0.75527462 0.69298218 0.44359033 -0.91849082 0.63404576 -0.11154952
[67] -0.45571389 1.59266502 -0.38776095 -0.90121392 0.47106856 -0.31658369
[73] -0.64509246 0.63684779 0.83135077 0.52097225 1.30052020 -1.29865737
[79] -1.10895747 -0.17772828 0.33130899 0.53367063 -1.21314430 0.21733394
[85] -1.53105147 -0.35777755 -0.56094823 0.36383418 0.40418018 0.80473376
[91] -1.02523060 -0.10855403 -1.41212023 0.29152993 -1.65252739 0.32476861
[97] 1.76232428 -0.79342918 -0.46907805 2.04295520
> colMedians(tmp)
[1] -0.35372554 -0.29007026 0.92554368 0.05556540 -1.02160988 -0.28154309
[7] -0.41064711 -0.46217719 -0.90785963 0.73112971 1.15118884 -0.23025444
[13] 0.82961279 4.42706155 2.00054918 -0.07003976 1.06148460 -1.60164257
[19] 0.13148942 0.71655102 1.83470161 -0.54355468 -0.07714368 -1.27157085
[25] -0.07535437 0.64532799 -0.23313105 1.39806869 0.92995469 -0.85128543
[31] 0.03657897 -1.06443463 -0.55840876 1.48287246 1.01953658 -1.91446436
[37] -0.18670163 -0.98494413 0.16089328 -0.45468447 0.50127449 -0.37578400
[43] -0.29116869 -1.53967119 0.25345017 0.35654935 -1.27121415 1.47820134
[49] -1.61020436 0.30443821 -0.58313458 1.32726755 1.20490422 1.46760953
[55] -1.45343125 -0.39679665 0.56990150 -1.47876553 -0.25635019 1.08194751
[61] 0.75527462 0.69298218 0.44359033 -0.91849082 0.63404576 -0.11154952
[67] -0.45571389 1.59266502 -0.38776095 -0.90121392 0.47106856 -0.31658369
[73] -0.64509246 0.63684779 0.83135077 0.52097225 1.30052020 -1.29865737
[79] -1.10895747 -0.17772828 0.33130899 0.53367063 -1.21314430 0.21733394
[85] -1.53105147 -0.35777755 -0.56094823 0.36383418 0.40418018 0.80473376
[91] -1.02523060 -0.10855403 -1.41212023 0.29152993 -1.65252739 0.32476861
[97] 1.76232428 -0.79342918 -0.46907805 2.04295520
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.3537255 -0.2900703 0.9255437 0.0555654 -1.02161 -0.2815431 -0.4106471
[2,] -0.3537255 -0.2900703 0.9255437 0.0555654 -1.02161 -0.2815431 -0.4106471
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.4621772 -0.9078596 0.7311297 1.151189 -0.2302544 0.8296128 4.427062
[2,] -0.4621772 -0.9078596 0.7311297 1.151189 -0.2302544 0.8296128 4.427062
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 2.000549 -0.07003976 1.061485 -1.601643 0.1314894 0.716551 1.834702
[2,] 2.000549 -0.07003976 1.061485 -1.601643 0.1314894 0.716551 1.834702
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.5435547 -0.07714368 -1.271571 -0.07535437 0.645328 -0.233131 1.398069
[2,] -0.5435547 -0.07714368 -1.271571 -0.07535437 0.645328 -0.233131 1.398069
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.9299547 -0.8512854 0.03657897 -1.064435 -0.5584088 1.482872 1.019537
[2,] 0.9299547 -0.8512854 0.03657897 -1.064435 -0.5584088 1.482872 1.019537
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -1.914464 -0.1867016 -0.9849441 0.1608933 -0.4546845 0.5012745 -0.375784
[2,] -1.914464 -0.1867016 -0.9849441 0.1608933 -0.4546845 0.5012745 -0.375784
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.2911687 -1.539671 0.2534502 0.3565493 -1.271214 1.478201 -1.610204
[2,] -0.2911687 -1.539671 0.2534502 0.3565493 -1.271214 1.478201 -1.610204
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.3044382 -0.5831346 1.327268 1.204904 1.46761 -1.453431 -0.3967967
[2,] 0.3044382 -0.5831346 1.327268 1.204904 1.46761 -1.453431 -0.3967967
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.5699015 -1.478766 -0.2563502 1.081948 0.7552746 0.6929822 0.4435903
[2,] 0.5699015 -1.478766 -0.2563502 1.081948 0.7552746 0.6929822 0.4435903
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -0.9184908 0.6340458 -0.1115495 -0.4557139 1.592665 -0.387761 -0.9012139
[2,] -0.9184908 0.6340458 -0.1115495 -0.4557139 1.592665 -0.387761 -0.9012139
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 0.4710686 -0.3165837 -0.6450925 0.6368478 0.8313508 0.5209723 1.30052
[2,] 0.4710686 -0.3165837 -0.6450925 0.6368478 0.8313508 0.5209723 1.30052
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -1.298657 -1.108957 -0.1777283 0.331309 0.5336706 -1.213144 0.2173339
[2,] -1.298657 -1.108957 -0.1777283 0.331309 0.5336706 -1.213144 0.2173339
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -1.531051 -0.3577776 -0.5609482 0.3638342 0.4041802 0.8047338 -1.025231
[2,] -1.531051 -0.3577776 -0.5609482 0.3638342 0.4041802 0.8047338 -1.025231
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.108554 -1.41212 0.2915299 -1.652527 0.3247686 1.762324 -0.7934292
[2,] -0.108554 -1.41212 0.2915299 -1.652527 0.3247686 1.762324 -0.7934292
[,99] [,100]
[1,] -0.469078 2.042955
[2,] -0.469078 2.042955
>
>
> Max(tmp2)
[1] 2.494535
> Min(tmp2)
[1] -2.813178
> mean(tmp2)
[1] -0.1272505
> Sum(tmp2)
[1] -12.72505
> Var(tmp2)
[1] 1.190691
>
> rowMeans(tmp2)
[1] -2.322851566 1.263776045 -1.389112472 0.885519071 -1.653302253
[6] 0.550540132 0.974293246 -1.170477143 2.494535249 -0.313098109
[11] -1.209096072 -0.724390537 0.279883730 -0.005488819 2.165525907
[16] -0.376846526 0.433949756 1.028774845 -0.174202633 -0.129814478
[21] 0.233909334 2.311376848 -0.004872179 -0.617041763 -0.739248325
[26] -0.582441512 -0.971398243 -0.807512660 -0.399011917 1.183677606
[31] -0.517236396 -0.685306530 -0.105320377 -1.053521812 -1.004754192
[36] 0.084322951 -0.352593756 -1.821793935 0.904754700 1.228891989
[41] 0.961618871 0.017718147 1.174617368 -1.160721186 -0.227711992
[46] -1.363337262 -0.067553192 -0.019779286 -0.058889827 -2.130300339
[51] 1.602501014 -0.530423851 0.305155488 0.173278998 -0.390468021
[56] -1.028257957 0.392945458 -1.104933226 0.733485082 -0.177873843
[61] 0.369632874 -0.157285070 -0.717661797 -1.949710738 0.792914734
[66] 2.397018313 -0.244752002 0.309908858 -1.466595548 0.314994112
[71] -0.114702488 1.302258641 -1.260391956 -1.674593983 -1.065821559
[76] -0.376842057 -1.306664698 -0.354326563 -0.256723162 -1.004638563
[81] 1.562055253 -0.080580097 0.814533691 -0.734973324 -1.499627768
[86] 1.548421849 1.082379461 -0.633750968 -2.813177735 -0.388211324
[91] 2.460949288 -1.059632129 -0.818116264 0.753953178 0.250939384
[96] -0.356357980 0.945461607 -1.994068531 0.265076311 0.439591033
> rowSums(tmp2)
[1] -2.322851566 1.263776045 -1.389112472 0.885519071 -1.653302253
[6] 0.550540132 0.974293246 -1.170477143 2.494535249 -0.313098109
[11] -1.209096072 -0.724390537 0.279883730 -0.005488819 2.165525907
[16] -0.376846526 0.433949756 1.028774845 -0.174202633 -0.129814478
[21] 0.233909334 2.311376848 -0.004872179 -0.617041763 -0.739248325
[26] -0.582441512 -0.971398243 -0.807512660 -0.399011917 1.183677606
[31] -0.517236396 -0.685306530 -0.105320377 -1.053521812 -1.004754192
[36] 0.084322951 -0.352593756 -1.821793935 0.904754700 1.228891989
[41] 0.961618871 0.017718147 1.174617368 -1.160721186 -0.227711992
[46] -1.363337262 -0.067553192 -0.019779286 -0.058889827 -2.130300339
[51] 1.602501014 -0.530423851 0.305155488 0.173278998 -0.390468021
[56] -1.028257957 0.392945458 -1.104933226 0.733485082 -0.177873843
[61] 0.369632874 -0.157285070 -0.717661797 -1.949710738 0.792914734
[66] 2.397018313 -0.244752002 0.309908858 -1.466595548 0.314994112
[71] -0.114702488 1.302258641 -1.260391956 -1.674593983 -1.065821559
[76] -0.376842057 -1.306664698 -0.354326563 -0.256723162 -1.004638563
[81] 1.562055253 -0.080580097 0.814533691 -0.734973324 -1.499627768
[86] 1.548421849 1.082379461 -0.633750968 -2.813177735 -0.388211324
[91] 2.460949288 -1.059632129 -0.818116264 0.753953178 0.250939384
[96] -0.356357980 0.945461607 -1.994068531 0.265076311 0.439591033
> rowVars(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowSd(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowMax(tmp2)
[1] -2.322851566 1.263776045 -1.389112472 0.885519071 -1.653302253
[6] 0.550540132 0.974293246 -1.170477143 2.494535249 -0.313098109
[11] -1.209096072 -0.724390537 0.279883730 -0.005488819 2.165525907
[16] -0.376846526 0.433949756 1.028774845 -0.174202633 -0.129814478
[21] 0.233909334 2.311376848 -0.004872179 -0.617041763 -0.739248325
[26] -0.582441512 -0.971398243 -0.807512660 -0.399011917 1.183677606
[31] -0.517236396 -0.685306530 -0.105320377 -1.053521812 -1.004754192
[36] 0.084322951 -0.352593756 -1.821793935 0.904754700 1.228891989
[41] 0.961618871 0.017718147 1.174617368 -1.160721186 -0.227711992
[46] -1.363337262 -0.067553192 -0.019779286 -0.058889827 -2.130300339
[51] 1.602501014 -0.530423851 0.305155488 0.173278998 -0.390468021
[56] -1.028257957 0.392945458 -1.104933226 0.733485082 -0.177873843
[61] 0.369632874 -0.157285070 -0.717661797 -1.949710738 0.792914734
[66] 2.397018313 -0.244752002 0.309908858 -1.466595548 0.314994112
[71] -0.114702488 1.302258641 -1.260391956 -1.674593983 -1.065821559
[76] -0.376842057 -1.306664698 -0.354326563 -0.256723162 -1.004638563
[81] 1.562055253 -0.080580097 0.814533691 -0.734973324 -1.499627768
[86] 1.548421849 1.082379461 -0.633750968 -2.813177735 -0.388211324
[91] 2.460949288 -1.059632129 -0.818116264 0.753953178 0.250939384
[96] -0.356357980 0.945461607 -1.994068531 0.265076311 0.439591033
> rowMin(tmp2)
[1] -2.322851566 1.263776045 -1.389112472 0.885519071 -1.653302253
[6] 0.550540132 0.974293246 -1.170477143 2.494535249 -0.313098109
[11] -1.209096072 -0.724390537 0.279883730 -0.005488819 2.165525907
[16] -0.376846526 0.433949756 1.028774845 -0.174202633 -0.129814478
[21] 0.233909334 2.311376848 -0.004872179 -0.617041763 -0.739248325
[26] -0.582441512 -0.971398243 -0.807512660 -0.399011917 1.183677606
[31] -0.517236396 -0.685306530 -0.105320377 -1.053521812 -1.004754192
[36] 0.084322951 -0.352593756 -1.821793935 0.904754700 1.228891989
[41] 0.961618871 0.017718147 1.174617368 -1.160721186 -0.227711992
[46] -1.363337262 -0.067553192 -0.019779286 -0.058889827 -2.130300339
[51] 1.602501014 -0.530423851 0.305155488 0.173278998 -0.390468021
[56] -1.028257957 0.392945458 -1.104933226 0.733485082 -0.177873843
[61] 0.369632874 -0.157285070 -0.717661797 -1.949710738 0.792914734
[66] 2.397018313 -0.244752002 0.309908858 -1.466595548 0.314994112
[71] -0.114702488 1.302258641 -1.260391956 -1.674593983 -1.065821559
[76] -0.376842057 -1.306664698 -0.354326563 -0.256723162 -1.004638563
[81] 1.562055253 -0.080580097 0.814533691 -0.734973324 -1.499627768
[86] 1.548421849 1.082379461 -0.633750968 -2.813177735 -0.388211324
[91] 2.460949288 -1.059632129 -0.818116264 0.753953178 0.250939384
[96] -0.356357980 0.945461607 -1.994068531 0.265076311 0.439591033
>
> colMeans(tmp2)
[1] -0.1272505
> colSums(tmp2)
[1] -12.72505
> colVars(tmp2)
[1] 1.190691
> colSd(tmp2)
[1] 1.091188
> colMax(tmp2)
[1] 2.494535
> colMin(tmp2)
[1] -2.813178
> colMedians(tmp2)
[1] -0.1760382
> colRanges(tmp2)
[,1]
[1,] -2.813178
[2,] 2.494535
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] -1.951250 -5.876568 -8.765473 -1.268653 5.378153 -2.855139 2.607019
[8] 3.014860 -3.043780 -1.214596
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.8377701
[2,] -0.7831243
[3,] -0.2072929
[4,] 0.3235445
[5,] 1.1733004
>
> rowApply(tmp,sum)
[1] -0.07866149 -0.23271339 2.72625806 2.85270423 -1.95582582 -2.45544905
[7] -2.50642977 -5.70228312 -0.68110867 -5.94191757
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 6 5 5 3 9 2 10 9 2 3
[2,] 4 1 3 2 2 7 6 8 9 1
[3,] 2 3 2 6 1 1 8 5 1 8
[4,] 1 9 8 5 3 8 5 4 8 9
[5,] 5 10 9 10 8 4 1 6 10 10
[6,] 8 6 7 4 5 3 9 1 4 7
[7,] 9 7 10 8 7 5 7 2 6 6
[8,] 10 8 6 9 4 6 3 10 5 5
[9,] 3 4 1 1 10 10 4 3 3 4
[10,] 7 2 4 7 6 9 2 7 7 2
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 3.6498663 -1.5280498 -0.1624128 -2.3312289 -0.4112826 2.2418377
[7] 0.6248729 -3.2571420 -0.2221779 2.2712194 0.3507902 -1.2909674
[13] -4.2210704 6.5241284 3.1670856 -1.9648888 0.4727785 0.4774808
[19] -3.6003602 1.6977354
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.30117441
[2,] 0.07449434
[3,] 0.73658386
[4,] 1.22222799
[5,] 1.91773449
>
> rowApply(tmp,sum)
[1] 0.1707623 7.7226675 1.5105680 -1.4010239 -5.5147595
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 20 6 15 12 20
[2,] 14 14 1 9 2
[3,] 13 12 7 11 5
[4,] 8 5 19 1 8
[5,] 1 15 5 16 12
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1.91773449 0.5809791 0.2288273 -0.8167024 -1.566656707 -0.3054456
[2,] -0.30117441 0.8976930 0.8763748 -0.5209984 0.999638633 0.2670980
[3,] 0.73658386 -1.6405496 -0.3807326 1.5537866 -0.431339542 0.6155940
[4,] 0.07449434 -0.2528720 -0.1198427 -1.9738265 0.579390363 2.6278753
[5,] 1.22222799 -1.1133004 -0.7670397 -0.5734881 0.007684665 -0.9632840
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 1.35977870 -0.8474206 -0.9061173 1.3535482 -0.03486871 -0.883367378
[2,] 0.06919985 -0.8434886 0.4424022 1.3204231 0.49810618 0.893554722
[3,] -0.29930351 -1.1050990 0.7532877 0.2054953 -1.17274605 0.005861141
[4,] -0.81974731 0.2125003 0.1877681 -0.2374369 0.60715657 -1.461269722
[5,] 0.31494520 -0.6736340 -0.6995187 -0.3708104 0.45314219 0.154253818
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.7471538 1.6546551 1.4257308 -0.04143667 -1.500628215 -0.89824344
[2,] -1.1748523 1.8044904 1.2150147 -1.58146190 1.310836651 0.64525405
[3,] -0.1700695 2.2979381 -0.9394818 -0.09143393 0.007516485 1.09229678
[4,] -1.0406008 0.3764319 0.7452351 -0.28951503 1.031618797 -0.29021038
[5,] -2.5827016 0.3906129 0.7205868 0.03895877 -0.376565260 -0.07161616
[,19] [,20]
[1,] -0.9568743 -0.3398839
[2,] -0.7965452 1.7011019
[3,] -0.3966517 0.8696151
[4,] -0.5891911 -0.7689823
[5,] -0.8610980 0.2358845
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 652 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 565 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 0.7621278 2.009707 -0.09373391 0.8589028 1.145404 -1.474786 0.03543875
col8 col9 col10 col11 col12 col13 col14
row1 0.0301536 0.02254976 -0.4524916 -1.350705 -0.2382903 -0.7347332 0.1483075
col15 col16 col17 col18 col19 col20
row1 0.2358228 0.5962439 0.6932895 0.1908814 0.1680347 0.6693557
> tmp[,"col10"]
col10
row1 -0.4524916
row2 0.3190536
row3 -0.8779576
row4 0.4831841
row5 1.6110553
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 0.7621278 2.009707 -0.09373391 0.8589028 1.1454045 -1.4747859
row5 -0.4586562 0.241687 0.76435220 -0.7016787 0.4526319 0.2831794
col7 col8 col9 col10 col11 col12
row1 0.03543875 0.0301536 0.02254976 -0.4524916 -1.3507051 -0.2382903
row5 -0.02971774 0.2989580 0.99870641 1.6110553 -0.5194621 -0.6953614
col13 col14 col15 col16 col17 col18 col19
row1 -0.7347332 0.1483075 0.2358228 0.5962439 0.6932895 0.1908814 0.1680347
row5 -1.0101870 -0.1690369 -1.2167059 0.1797960 0.2141780 1.6787249 -1.8228294
col20
row1 0.6693557
row5 -0.5772010
> tmp[,c("col6","col20")]
col6 col20
row1 -1.4747859 0.6693557
row2 -0.7161467 -0.2336857
row3 -1.3217285 0.9756234
row4 -1.2622509 -0.7913239
row5 0.2831794 -0.5772010
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -1.4747859 0.6693557
row5 0.2831794 -0.5772010
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.80306 50.49877 50.25618 50.2705 50.47828 105.648 50.50714 50.82928
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.18858 49.19748 50.3865 50.93311 49.9415 48.56421 49.62051 50.85072
col17 col18 col19 col20
row1 50.35323 50.75006 48.18643 106.09
> tmp[,"col10"]
col10
row1 49.19748
row2 32.22572
row3 30.68160
row4 29.43431
row5 49.49047
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.80306 50.49877 50.25618 50.27050 50.47828 105.6480 50.50714 50.82928
row5 48.42551 49.78964 48.55825 51.32384 50.69606 105.4028 50.54365 49.65262
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.18858 49.19748 50.38650 50.93311 49.94150 48.56421 49.62051 50.85072
row5 50.29051 49.49047 50.28596 51.10185 49.62444 52.65147 49.40856 49.45757
col17 col18 col19 col20
row1 50.35323 50.75006 48.18643 106.0900
row5 49.69936 50.28990 51.36972 107.5033
> tmp[,c("col6","col20")]
col6 col20
row1 105.64797 106.08996
row2 76.13466 73.39854
row3 73.45401 75.32001
row4 75.35511 75.02095
row5 105.40278 107.50332
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.6480 106.0900
row5 105.4028 107.5033
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.6480 106.0900
row5 105.4028 107.5033
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.15679857
[2,] -1.33394409
[3,] -0.47560220
[4,] -0.00561664
[5,] 1.02519088
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.01610403 0.0380109
[2,] 0.48729076 1.1561005
[3,] -1.20992452 -0.2112349
[4,] -0.78699809 -0.6056557
[5,] -1.49630690 1.0287880
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -1.9794430 0.2907842
[2,] 0.2777679 -0.6039315
[3,] 0.9912218 -0.8768663
[4,] -1.2192087 1.1854351
[5,] -0.9442313 0.7129595
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -1.979443
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -1.9794430
[2,] 0.2777679
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row3 -1.205952 0.96005025 -0.1882272 -0.8417193 0.3434165 1.2226758
row1 1.012711 -0.03063218 0.1825827 -1.5143666 1.9213333 -0.1072602
[,7] [,8] [,9] [,10] [,11] [,12]
row3 -0.9338532 0.4196072 -0.22467844 -0.4811634 -0.5139877 1.1088471
row1 0.7051393 -0.2414822 -0.04556853 -0.8386631 -0.1467817 0.2179852
[,13] [,14] [,15] [,16] [,17] [,18] [,19]
row3 -0.6222017 0.2070094 0.0434427 0.7103283 -0.1081128 0.2463430 -1.3287344
row1 -0.2063670 0.1203139 -1.5322498 -1.7495250 0.7014477 0.8970485 0.9414966
[,20]
row3 -0.5411942
row1 -1.4608832
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -1.539998 -0.03115737 -0.9832776 -1.272729 0.03577394 -0.4006178 1.994436
[,8] [,9] [,10]
row2 1.120634 0.7123749 -2.071103
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.1491061 -0.8335382 0.1674976 1.232199 0.3535639 1.06253 -0.7831958
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 0.05533478 0.1013905 1.137103 -1.459573 -0.3671958 0.08481838 0.1515641
[,15] [,16] [,17] [,18] [,19] [,20]
row5 2.025188 -0.3085447 -0.5393302 -2.738031 -0.567952 1.394751
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> colnames(tmp) <- NULL
> rownames(tmp) <- NULL
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
> dimnames(tmp) <- NULL
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
> dimnames(tmp) <- NULL
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
NULL
>
> dimnames(tmp) <- list(NULL,c(colnames(tmp,do.NULL=FALSE)))
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
>
> ###
> ### Testing logical indexing
> ###
> ###
>
> tmp <- createBufferedMatrix(230,15)
> tmp[1:230,1:15] <- rnorm(230*15)
> x <-tmp[1:230,1:15]
>
> for (rep in 1:10){
+ which.cols <- sample(c(TRUE,FALSE),15,replace=T)
+ which.rows <- sample(c(TRUE,FALSE),230,replace=T)
+
+ if (!all(tmp[which.rows,which.cols] == x[which.rows,which.cols])){
+ stop("No agreement when logical indexing\n")
+ }
+
+ if (!all(subBufferedMatrix(tmp,,which.cols)[,1:sum(which.cols)] == x[,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix cols\n")
+ }
+ if (!all(subBufferedMatrix(tmp,which.rows,)[1:sum(which.rows),] == x[which.rows,])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows\n")
+ }
+
+
+ if (!all(subBufferedMatrix(tmp,which.rows,which.cols)[1:sum(which.rows),1:sum(which.cols)]== x[which.rows,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows and columns\n")
+ }
+ }
>
>
> ##
> ## Test the ReadOnlyMode
> ##
>
> ReadOnlyMode(tmp)
<pointer: 0x5ff3d81f4ca0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3d92fe321d04da"
[2] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3d92fe2e50d9e0"
[3] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3d92fe47f1fe21"
[4] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3d92fe4aca7fe3"
[5] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3d92fe4942eb9c"
[6] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3d92fe3bd06cd7"
[7] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3d92fe7b06dde5"
[8] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3d92fe31693811"
[9] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3d92fe7350b769"
[10] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3d92fe22f384fc"
[11] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3d92fe59c30ce7"
[12] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3d92fe33d59073"
[13] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3d92fe4695f169"
[14] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3d92fe49de7f40"
[15] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3d92fe1777eb9e"
>
>
> ### testing coercion functions
> ###
>
> tmp <- as(tmp,"matrix")
> tmp <- as(tmp,"BufferedMatrix")
>
>
>
> ### testing whether can move storage from one location to another
>
> MoveStorageDirectory(tmp,"NewDirectory",full.path=FALSE)
<pointer: 0x5ff3d8aa0350>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x5ff3d8aa0350>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x5ff3d8aa0350>
> rowMedians(tmp)
[1] 0.0435344076 0.1919252817 0.2802463087 0.4502154319 0.0250254867
[6] 0.1688918545 0.0365855776 -0.5544747879 0.0961555594 -0.5768535235
[11] 0.0275406240 -0.1766614635 -0.1774985846 0.0841824287 0.2872231580
[16] 0.2389324171 -0.0193184887 0.7071367866 -0.0010114812 -0.3885742363
[21] 0.2914183732 -0.1090304295 0.1178283270 -0.3091616944 -0.1253245169
[26] 0.1829306440 0.4981435211 -0.2864284181 -0.1070815197 0.1874483505
[31] 0.3097013342 0.0193935589 0.0438076231 -0.0307168503 -0.1790407610
[36] -0.6721780924 0.1085848736 0.1182269835 0.1677517894 -0.2930815930
[41] -0.0356350664 -0.2971133346 0.6121667203 -0.4824848585 -0.0240971875
[46] 0.9390079182 -0.0783333749 -0.2952458905 -0.1414815767 -0.1712472763
[51] 0.2805441871 -0.1577580209 -0.0424329993 -0.4954347459 -0.2967391079
[56] 0.1567908273 0.4269397579 -0.1457180299 0.6026191598 0.2386088939
[61] 0.1426748246 -0.2977163112 -0.0543316043 0.2871022705 -0.1728801246
[66] -0.5318116677 0.4517338302 -0.1747713721 -0.2301664150 -0.0919047103
[71] -0.0766659739 -0.4215929054 0.0191060016 -0.0464983130 -0.0655134203
[76] 0.0042570613 0.2466717010 -0.1745652427 0.2793686620 -0.3386656097
[81] -0.1717059702 0.0354511746 -0.6194632286 0.3809354348 -0.2696090117
[86] 0.0333339562 -0.6343116987 0.0021860093 -0.2900072495 -0.1479091214
[91] 0.1574285946 -0.6356339606 0.1867989161 -0.3531432230 -0.1274464699
[96] -0.1506321261 -0.1469131473 -0.1627978805 0.3182331671 -0.0478669682
[101] 0.2365254745 0.2848953324 -0.5275854166 0.2916345771 0.0959814091
[106] -0.0994495644 -0.0422849264 0.4900072553 -0.1207708425 -0.3127430123
[111] 0.2567897236 0.2042841436 0.0203999538 -0.0167769397 -0.5087818635
[116] -0.4297753106 -0.3384605934 0.2547867572 0.0400889108 -0.2917118063
[121] 0.3247227524 -0.3166948778 0.1648104032 0.1292559806 0.3009328593
[126] -0.4222790135 -0.2846938935 0.3972253803 0.0432840985 -0.1402982010
[131] -0.1484592052 1.1119463979 0.0539646468 -0.0774542843 -0.0008546259
[136] 0.3769162942 -0.1445725041 -0.0893128155 -0.2807397350 0.1154541140
[141] 0.2572996428 0.4154320864 -0.3089630505 0.6046840885 -0.3371066468
[146] -0.1351854974 0.2683645952 -0.0225205079 -0.1839990389 0.3146372954
[151] -0.1691195208 0.0173345906 0.1610076590 0.1052116547 0.3637841959
[156] -0.1486106060 -0.1360669502 0.0585039880 -0.1701420469 -0.0853967354
[161] 0.0467565765 0.1333300889 0.0487782922 -0.0023114834 0.0513761766
[166] 0.3286030900 -0.1508188822 0.2379403963 0.0424561848 0.5229714439
[171] 0.0206084959 -0.0809496978 0.3382615663 0.2159987918 0.4253455833
[176] 0.4250497998 -0.3115100853 0.7038651051 0.1124958418 0.0807447733
[181] -0.1132840328 -0.2817126235 0.0948891088 0.1565387267 0.1040402631
[186] 0.3414198439 -0.3272650328 0.0421442460 0.2546950243 -0.0695239841
[191] -0.6733631404 0.5971604040 -0.0440911038 -0.7065238715 0.0056620114
[196] -0.0635576706 -0.0853999056 0.5991900783 -0.7584706244 0.1007574221
[201] -0.0255017940 0.0497306303 -0.0252142117 -0.1491623123 0.5368114525
[206] -0.1612853183 0.0892722679 -0.0051149701 0.0881282141 0.1009888723
[211] -0.4339336304 0.3656647885 -0.5442520383 0.0796470581 -0.4767655896
[216] 0.2105117532 -0.0304627318 0.1143714695 -0.3541176968 0.6018966970
[221] -0.2369410738 -0.0995752638 -0.0168170576 0.5773593392 0.1605086372
[226] -0.1366605904 -0.3328882633 -0.0695828207 0.2120815713 -0.4213358081
>
> proc.time()
user system elapsed
1.274 0.643 1.907
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> prefix <- "dbmtest"
> directory <- getwd()
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x575e0d54c370>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x575e0d54c370>
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x575e0d54c370>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000 0.000000 0.000000 0.000000 0.000000
<pointer: 0x575e0d54c370>
> rm(P)
>
> #P <- .Call("R_bm_Destroy",P)
> #.Call("R_bm_Destroy",P)
> #.Call("R_bm_Test_C",P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 0
Buffer Rows: 1
Buffer Cols: 1
Printing Values
<pointer: 0x575e0d5341c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x575e0d5341c0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 1
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000
0.000000
0.000000
0.000000
0.000000
<pointer: 0x575e0d5341c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x575e0d5341c0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x575e0d5341c0>
> rm(P)
>
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x575e0d817120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x575e0d817120>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x575e0d817120>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x575e0d817120>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x575e0d817120>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x575e0d817120>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x575e0d817120>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x575e0d817120>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x575e0d817120>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x575e0c567390>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x575e0c567390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x575e0c567390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x575e0c567390>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile3d9383389b0c0d" "BufferedMatrixFile3d938368f6e42e"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile3d9383389b0c0d" "BufferedMatrixFile3d938368f6e42e"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x575e0c45e3d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x575e0c45e3d0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x575e0c45e3d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x575e0c45e3d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x575e0c45e3d0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x575e0c45e3d0>
> .Call("R_bm_isRowMode",P)
[1] FALSE
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x575e0df93fa0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x575e0df93fa0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x575e0df93fa0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x575e0df93fa0>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x575e0c76bff0>
> .Call("R_bm_getValue",P,3,3)
[1] 6
>
> .Call("R_bm_getValue",P,100000,10000)
[1] NA
> .Call("R_bm_setValue",P,3,3,12345.0)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 12345.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x575e0c76bff0>
> rm(P)
>
> proc.time()
user system elapsed
0.274 0.051 0.305
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.245 0.038 0.272